› 8r57

Electron Microscopy
2.55Å resolution

CryoEM structure of wheat 40S ribosomal subunit, head domain

Released:
DOI: 10.2210/pdb8r57/pdb
PDB entry 8r57 coloured by chain, front view.
PDB entry 8r57 coloured by chain, side view.
PDB entry 8r57 coloured by chain, top view.
Source organism: Triticum aestivum
Primary publication:
High-Resolution Structure and Internal Mobility of a Plant 40S Ribosomal Subunit.
Kravchenko OV, Baymukhametov TN, Afonina ZA, Vassilenko KS
Int J Mol Sci 24 (2023)
PMID: 38139282
Related structures: EMD-18903

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domain:

Structure analysis Details

Assembly composition:
hetero hexadecamer (preferred)
PDBe Complex ID:
PDB-CPX-237514 (preferred)
Entry contents:
15 distinct polypeptide molecules
1 distinct RNA molecule
Macromolecules (16 distinct):
Plectin/eS10 N-terminal domain-containing protein Chain: K
Molecule details ›
Chain: K
Length: 188 amino acids
Theoretical weight: 20.46 KDa
Source organism: Triticum aestivum
UniProt:
  • Canonical: W5AUH7 (Residues: 1-188; Coverage: 100%)
Gene name: CFC21_017397
Sequence domains: Plectin/S10 domain
40S ribosomal protein S12 Chain: M
Molecule details ›
Chain: M
Length: 144 amino acids
Theoretical weight: 15.36 KDa
Source organism: Triticum aestivum
UniProt:
  • Canonical: W5FEZ3 (Residues: 1-144; Coverage: 100%)
Gene names: CFC21_073837, CFC21_079859
Sequence domains: Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
30S ribosomal protein S3, chloroplastic Chain: F
Molecule details ›
Chain: F
Length: 227 amino acids
Theoretical weight: 25.4 KDa
Source organism: Triticum aestivum
UniProt:
  • Canonical: W5I1R7 (Residues: 1-227; Coverage: 100%)
Gene names: CFC21_034353, CFC21_034354, CFC21_109361
Sequence domains:
Small ribosomal subunit protein uS7c Chain: P
Molecule details ›
Chain: P
Length: 200 amino acids
Theoretical weight: 22.35 KDa
Source organism: Triticum aestivum
UniProt:
  • Canonical: W5D067 (Residues: 1-200; Coverage: 100%)
Gene names: CFC21_039914, TRAES_3BF058200010CFD_c1
Sequence domains: Ribosomal protein S7p/S5e
40S ribosomal protein S16 Chain: Q
Molecule details ›
Chain: Q
Length: 149 amino acids
Theoretical weight: 16.86 KDa
Source organism: Triticum aestivum
UniProt:
  • Canonical: W5DS33 (Residues: 1-149; Coverage: 100%)
Gene names: CFC21_052701, CFC21_057238, CFC21_057239, CFC21_061195, CFC21_061198
Sequence domains: Ribosomal protein S9/S16
Small ribosomal subunit protein uS10 domain-containing protein Chain: U
Molecule details ›
Chain: U
Length: 127 amino acids
Theoretical weight: 14.13 KDa
Source organism: Triticum aestivum
UniProt:
  • Canonical: U5HTD8 (Residues: 1-127; Coverage: 100%)
Gene names: CFC21_019225, CFC21_019228, CFC21_019231, CFC21_019235, CFC21_054980, CFC21_107037, rps20
Sequence domains: Ribosomal protein S10p/S20e
40S ribosomal protein S19 Chain: T
Molecule details ›
Chain: T
Length: 155 amino acids
Theoretical weight: 17.1 KDa
Source organism: Triticum aestivum
UniProt:
  • Canonical: W5FWF5 (Residues: 1-155; Coverage: 100%)
Gene names: CFC21_065464, CFC21_076659
Sequence domains: Ribosomal protein S19e
40S ribosomal protein S25 Chain: Z
Molecule details ›
Chain: Z
Length: 108 amino acids
Theoretical weight: 12.09 KDa
Source organism: Triticum aestivum
UniProt:
  • Canonical: W5EP45 (Residues: 1-108; Coverage: 100%)
Gene names: CFC21_009979, CFC21_056005, CFC21_056010, CFC21_056015
Sequence domains: S25 ribosomal protein
40S ribosomal protein S28 Chain: c
Molecule details ›
Chain: c
Length: 65 amino acids
Theoretical weight: 7.48 KDa
Source organism: Triticum aestivum
UniProt:
  • Canonical: W5E8X2 (Residues: 1-65; Coverage: 100%)
Gene names: CFC21_038625, CFC21_038626, CFC21_050693, CFC21_052484, CFC21_052485, CFC21_061583
Sequence domains: Ribosomal protein S28e
Small ribosomal subunit protein uS14 Chain: d
Molecule details ›
Chain: d
Length: 56 amino acids
Theoretical weight: 6.39 KDa
Source organism: Triticum aestivum
UniProt:
  • Canonical: Q5I7K3 (Residues: 1-56; Coverage: 100%)
Gene name: RPS29
Sequence domains: Ribosomal protein S14p/S29e
Ribosomal protein RACK1 subfamily. WD repeat G protein beta family Chain: g
Molecule details ›
Chain: g
Length: 332 amino acids
Theoretical weight: 36.2 KDa
Source organism: Triticum aestivum
UniProt:
  • Canonical: W5D4F5 (Residues: 1-332; Coverage: 100%)
Gene names: CFC21_040720, CFC21_047775, TRAES_3BF007900030CFD_c1
Sequence domains: WD domain, G-beta repeat
Putative ribosomal protein S18 Chain: S
Molecule details ›
Chain: S
Length: 152 amino acids
Theoretical weight: 17.7 KDa
Source organism: Triticum aestivum
UniProt:
  • Canonical: Q8L806 (Residues: 1-152; Coverage: 100%)
Gene names: CFC21_068138, CFC21_073936, CFC21_099813
Sequence domains: Ribosomal protein S13/S18
40S ribosomal protein S15 Chain: R
Molecule details ›
Chain: R
Length: 153 amino acids
Theoretical weight: 17.3 KDa
Source organism: Triticum aestivum
UniProt:
  • Canonical: A0A3B6LV48 (Residues: 1-153; Coverage: 100%)
Gene name: CFC21_074055
Sequence domains: Ribosomal protein S19
40S ribosomal protein S17 Chain: h
Molecule details ›
Chain: h
Length: 143 amino acids
Theoretical weight: 16.48 KDa
Source organism: Triticum aestivum
UniProt:
  • Canonical: A0A3B5XY60 (Residues: 1-143; Coverage: 100%)
Sequence domains: Ribosomal S17
Ubiquitin-like domain-containing protein Chain: f
Molecule details ›
Chain: f
Length: 155 amino acids
Theoretical weight: 17.69 KDa
Source organism: Triticum aestivum
UniProt:
  • Canonical: W5A9E1 (Residues: 1-155; Coverage: 100%)
Gene names: CFC21_005988, CFC21_010768
Sequence domains:
RNA (458-MER) Chain: A
Molecule details ›
Chain: A
Length: 1810 nucleotides
Theoretical weight: 584.38 KDa
Sequence domains: Eukaryotic small subunit ribosomal RNA

Ligands and Environments

3 bound ligands:
Ligand MG 20 x MG
Ligand ZN 2 x ZN
Ligand K 6 x K
8 modified residues:
Ligand A2M 12 x A2M
Ligand PSU 41 x PSU
Ligand OMC 6 x OMC
Ligand OMU 10 x OMU
Ligand OMG 8 x OMG
Ligand 7MG 1 x 7MG
Ligand 6MZ 1 x 6MZ
Ligand MA6 2 x MA6

Experiments and Validation Details

Entry percentile scores
Resolution: 2.55Å
Relevant EMDB volumes: EMD-18903

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